SMTL ID : 8yh8.1

F1 domain of Non-catalytic site depleted and epsilon C-terminal domain deleted FoF1-ATPase from Bacillus PS3,under ATP saturated condition

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain D: T.165, R.191 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.165 MG.4: 2 residues within 4Å: Chain E: T.165 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain F: T.165 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.165

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 15 residues within 4Å: Chain C: S.339, R.340 Chain D: G.159, G.161, V.162, G.163, K.164, T.165, V.166, Y.341, F.414, A.417, F.420, T.421 Ligands: MG.1 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.159, D:G.161, D:V.162, D:G.163, D:K.164, D:T.165, D:T.165, D:V.166, D:Y.341, C:S.339 Salt bridges: D:K.164, C:R.340, C:R.340 pi-Stacking: D:Y.341, D:Y.341 ADP.3: 11 residues within 4Å: Chain E: G.161, V.162, G.163, K.164, T.165, V.166, Y.341, F.414, A.417, F.420 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.161, E:V.162, E:G.163, E:K.164, E:T.165, E:T.165, E:V.166 pi-Stacking: E:Y.341, E:Y.341

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 16 residues within 4Å: Chain B: I.310, S.311, R.340 Chain F: G.159, G.161, V.162, G.163, K.164, T.165, V.166, R.191, Y.341, F.414, A.417, F.420 Ligands: MG.6 17 PLIP interactions: 12 interactions with chain F, 5 interactions with chain B Hydrogen bonds: F:G.161, F:V.162, F:G.163, F:K.164, F:T.165, F:T.165, F:V.166, B:S.311, B:R.340 Salt bridges: F:K.164, F:K.164, F:R.191, B:R.340, B:R.340, B:R.340 pi-Stacking: F:Y.341, F:Y.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobayashi, R. et al., ADP-inhibited structure of non-catalytic site-depleted F o F 1 -ATPase from thermophilic Bacillus sp. PS-3. Biochim Biophys Acta Bioenerg (2025)

Release Date

2025-05-14

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

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